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Potassium in PDB 6dvn: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137, PDB code: 6dvn was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.550, 95.500, 98.250, 90.00, 98.60, 90.00
R / Rfree (%) 18.8 / 22.3

Other elements in 6dvn:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 (pdb code 6dvn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137, PDB code: 6dvn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 1 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:15.5
occ:1.00
O A:ASP612 2.7 14.6 1.0
O A:HIS614 2.7 12.6 1.0
OG A:SER633 2.8 9.7 1.0
O A:LEU634 2.8 14.4 1.0
O A:ASP610 2.8 11.9 1.0
OD1 A:ASP610 2.9 11.8 1.0
CG A:ASP610 3.2 14.4 1.0
C A:ASP610 3.6 13.1 1.0
C A:ASP612 3.7 13.0 1.0
C A:LEU634 3.7 14.0 1.0
C A:HIS614 3.7 12.1 1.0
CB A:ASP610 3.8 15.7 1.0
N A:ASP612 3.8 13.2 1.0
OD2 A:ASP610 3.8 13.1 1.0
CB A:SER633 3.8 15.3 1.0
N A:LEU634 3.9 12.8 1.0
CB A:HIS635 3.9 9.6 1.0
CA A:ASP612 4.1 12.7 1.0
CA A:SER633 4.2 13.2 1.0
CB A:ASP612 4.2 13.5 1.0
CA A:ASP610 4.3 15.0 1.0
C A:TRP611 4.3 13.9 1.0
CA A:HIS615 4.3 11.2 1.0
N A:TRP611 4.3 11.4 1.0
C A:SER633 4.4 14.8 1.0
N A:GLY616 4.4 10.8 1.0
CA A:HIS635 4.4 11.6 1.0
N A:HIS615 4.4 12.2 1.0
ND1 A:HIS635 4.4 11.8 1.0
CA A:TRP611 4.4 12.4 1.0
N A:HIS635 4.5 9.7 1.0
CA A:LEU634 4.5 14.5 1.0
N A:HIS614 4.5 12.5 1.0
O A:HOH905 4.6 12.1 1.0
CG A:HIS635 4.6 10.8 1.0
OH A:TYR631 4.7 18.1 1.0
C A:HIS615 4.7 13.2 1.0
CA A:HIS614 4.8 14.7 1.0
N A:VAL613 4.8 15.6 1.0
C A:VAL613 4.8 14.5 1.0
CE1 A:HIS573 4.9 17.8 1.0

Potassium binding site 2 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 2 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:19.3
occ:1.00
O A:PHE623 2.7 18.1 1.0
O A:VAL629 2.7 16.3 1.0
O A:HOH913 2.7 18.7 1.0
O A:TYR662 2.8 12.5 1.0
O A:HOH908 2.9 11.6 1.0
O A:ASP626 3.0 20.0 1.0
C A:TYR662 3.6 15.9 1.0
CB A:TYR662 3.7 14.6 1.0
C A:PHE623 3.7 14.4 1.0
CB A:PHE623 3.8 14.8 1.0
C A:VAL629 3.9 15.3 1.0
C A:ASP626 4.1 17.2 1.0
CA A:TYR662 4.3 15.1 1.0
N A:TYR631 4.3 13.4 1.0
CA A:PHE623 4.4 20.9 1.0
N A:ASN663 4.5 14.1 1.0
CA A:LEU630 4.5 13.9 1.0
N A:ASP626 4.6 18.9 1.0
N A:LEU630 4.7 13.7 1.0
N A:GLU624 4.7 14.7 1.0
CB A:TYR631 4.7 9.7 1.0
CA A:ASP626 4.8 13.8 1.0
CA A:GLU624 4.8 16.3 1.0
CB A:ASP626 4.8 16.9 1.0
CA A:ASN663 4.8 14.2 1.0
CB A:ASN663 4.8 12.0 1.0
O A:GLU624 4.8 15.3 1.0
C A:LEU630 4.8 11.0 1.0
C A:GLU624 4.9 17.6 1.0
O A:GLY659 4.9 16.8 1.0
CG A:TYR662 4.9 16.8 1.0
CA A:VAL629 5.0 14.2 1.0
OD1 A:ASN663 5.0 15.7 1.0

Potassium binding site 3 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 3 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:13.8
occ:1.00
O B:ASP612 2.7 10.5 1.0
O B:HIS614 2.8 11.6 1.0
O B:ASP610 2.8 7.0 1.0
O B:LEU634 2.8 9.8 1.0
OG B:SER633 2.8 8.1 1.0
OD1 B:ASP610 2.9 12.0 1.0
CG B:ASP610 3.2 15.1 1.0
C B:ASP610 3.5 10.1 1.0
C B:ASP612 3.7 8.9 1.0
C B:LEU634 3.7 10.6 1.0
CB B:ASP610 3.7 11.5 1.0
C B:HIS614 3.7 12.1 1.0
N B:ASP612 3.8 10.6 1.0
OD2 B:ASP610 3.8 15.9 1.0
N B:LEU634 3.9 9.6 1.0
CB B:SER633 3.9 13.1 1.0
CB B:HIS635 3.9 10.1 1.0
CA B:ASP612 4.2 9.8 1.0
CA B:ASP610 4.2 9.2 1.0
N B:TRP611 4.2 10.3 1.0
CA B:SER633 4.2 10.5 1.0
CA B:HIS615 4.2 10.7 1.0
C B:TRP611 4.2 14.3 1.0
CB B:ASP612 4.3 14.4 1.0
N B:HIS615 4.4 9.7 1.0
CA B:TRP611 4.4 9.9 1.0
C B:SER633 4.4 8.6 1.0
N B:GLY616 4.4 10.5 1.0
ND1 B:HIS635 4.4 12.4 1.0
CA B:HIS635 4.4 11.0 1.0
CA B:LEU634 4.5 9.2 1.0
N B:HIS635 4.5 10.2 1.0
N B:HIS614 4.5 11.0 1.0
CG B:HIS635 4.7 11.3 1.0
C B:HIS615 4.7 13.7 1.0
CA B:HIS614 4.8 12.9 1.0
OH B:TYR631 4.8 14.7 1.0
C B:VAL613 4.8 11.9 1.0
O B:HOH904 4.8 14.6 1.0
N B:VAL613 4.8 8.2 1.0
CE1 B:HIS573 4.9 14.4 1.0

Potassium binding site 4 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 4 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:17.1
occ:1.00
O B:PHE623 2.7 15.3 1.0
O B:VAL629 2.7 16.6 1.0
O B:HOH928 2.8 12.8 1.0
O B:TYR662 2.9 12.6 1.0
O B:HOH931 3.0 13.1 1.0
O B:ASP626 3.0 16.4 1.0
C B:PHE623 3.6 12.5 1.0
C B:TYR662 3.7 12.7 1.0
CB B:PHE623 3.7 11.4 1.0
CB B:TYR662 3.7 11.2 1.0
C B:VAL629 3.9 15.2 1.0
C B:ASP626 4.2 16.4 1.0
CA B:PHE623 4.3 13.1 1.0
N B:TYR631 4.3 13.3 1.0
CA B:TYR662 4.3 14.9 1.0
N B:ASN663 4.5 11.4 1.0
N B:GLU624 4.6 13.2 1.0
N B:ASP626 4.6 14.6 1.0
CA B:LEU630 4.6 10.3 1.0
CB B:TYR631 4.7 6.8 1.0
CA B:GLU624 4.7 18.1 1.0
N B:LEU630 4.7 13.8 1.0
CB B:ASN663 4.8 11.1 1.0
C B:GLU624 4.8 16.0 1.0
CA B:ASP626 4.8 14.6 1.0
O B:GLU624 4.8 12.8 1.0
CA B:ASN663 4.8 12.6 1.0
CB B:ASP626 4.9 24.8 1.0
C B:LEU630 4.9 9.8 1.0
O B:GLY659 4.9 19.8 1.0
CA B:VAL629 4.9 14.8 1.0
CG B:PHE623 5.0 14.6 1.0

Potassium binding site 5 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 5 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K802

b:14.1
occ:1.00
O C:ASP612 2.7 15.6 1.0
OG C:SER633 2.8 13.9 1.0
O C:ASP610 2.8 13.6 1.0
O C:LEU634 2.8 14.5 1.0
O C:HIS614 2.8 11.5 1.0
OD1 C:ASP610 2.9 14.5 1.0
CG C:ASP610 3.2 13.8 1.0
C C:ASP610 3.5 13.1 1.0
CB C:ASP610 3.7 16.1 1.0
C C:ASP612 3.7 16.5 1.0
OD2 C:ASP610 3.7 17.4 1.0
C C:LEU634 3.7 14.5 1.0
N C:ASP612 3.8 13.3 1.0
C C:HIS614 3.8 12.6 1.0
N C:LEU634 3.9 12.7 1.0
CB C:HIS635 3.9 9.7 1.0
CB C:SER633 4.0 15.7 1.0
CA C:ASP612 4.1 15.0 1.0
CA C:ASP610 4.2 11.2 1.0
ND1 C:HIS635 4.2 19.1 1.0
N C:TRP611 4.2 11.6 1.0
CB C:ASP612 4.2 15.9 1.0
C C:TRP611 4.2 16.8 1.0
CA C:HIS615 4.3 12.4 1.0
CA C:SER633 4.3 14.7 1.0
N C:HIS615 4.4 13.8 1.0
CA C:TRP611 4.4 17.1 1.0
C C:SER633 4.4 15.9 1.0
O C:HOH914 4.5 15.9 1.0
N C:GLY616 4.5 13.3 1.0
CA C:HIS635 4.5 11.9 1.0
CA C:LEU634 4.5 15.3 1.0
N C:HIS635 4.5 11.9 1.0
CG C:HIS635 4.5 14.2 1.0
N C:HIS614 4.5 13.5 1.0
C C:HIS615 4.8 14.2 1.0
OH C:TYR631 4.8 16.8 1.0
CA C:HIS614 4.8 14.4 1.0
N C:VAL613 4.8 15.1 1.0
C C:VAL613 4.8 13.3 1.0

Potassium binding site 6 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 6 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K803

b:22.5
occ:1.00
O C:PHE623 2.7 18.8 1.0
O C:VAL629 2.7 16.9 1.0
O C:HOH905 2.8 15.8 1.0
O C:ASP626 2.8 17.8 1.0
O C:TYR662 2.9 18.9 1.0
O C:HOH942 3.0 16.7 1.0
C C:TYR662 3.6 22.0 1.0
CB C:TYR662 3.6 18.3 1.0
C C:PHE623 3.7 16.2 1.0
CB C:PHE623 3.8 16.9 1.0
C C:VAL629 3.9 16.9 1.0
C C:ASP626 4.0 21.1 1.0
CA C:TYR662 4.2 17.6 1.0
N C:ASN663 4.4 18.8 1.0
CA C:PHE623 4.4 18.9 1.0
N C:TYR631 4.4 13.5 1.0
N C:ASP626 4.5 18.4 1.0
O C:GLU624 4.6 15.6 1.0
CA C:LEU630 4.6 14.9 1.0
N C:GLU624 4.6 16.4 1.0
CA C:GLU624 4.6 22.7 1.0
CA C:ASP626 4.6 21.6 1.0
C C:GLU624 4.7 18.6 1.0
CB C:ASP626 4.7 17.1 1.0
CB C:ASN663 4.7 13.5 1.0
N C:LEU630 4.7 14.2 1.0
CA C:ASN663 4.7 17.3 1.0
CB C:TYR631 4.8 12.1 1.0
O C:GLY659 4.9 19.1 1.0
CG C:TYR662 4.9 20.8 1.0
C C:LEU630 4.9 15.0 1.0
CA C:VAL629 5.0 20.0 1.0

Potassium binding site 7 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 7 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K802

b:12.8
occ:1.00
O D:ASP612 2.7 11.9 1.0
O D:ASP610 2.7 13.2 1.0
O D:HIS614 2.8 10.0 1.0
OG D:SER633 2.8 11.7 1.0
OD1 D:ASP610 2.9 15.9 1.0
O D:LEU634 2.9 16.4 1.0
CG D:ASP610 3.2 16.9 1.0
C D:ASP610 3.4 12.5 1.0
C D:ASP612 3.6 13.5 1.0
CB D:ASP610 3.7 12.8 1.0
N D:ASP612 3.7 13.4 1.0
OD2 D:ASP610 3.8 19.4 1.0
C D:HIS614 3.8 12.2 1.0
C D:LEU634 3.8 14.0 1.0
CB D:SER633 3.8 13.2 1.0
N D:LEU634 3.9 11.0 1.0
CB D:HIS635 4.0 7.8 1.0
CA D:ASP612 4.0 10.0 1.0
CB D:ASP612 4.1 13.0 1.0
CA D:ASP610 4.1 10.4 1.0
N D:TRP611 4.2 14.5 1.0
C D:TRP611 4.2 12.5 1.0
CA D:SER633 4.2 13.0 1.0
CA D:HIS615 4.3 14.3 1.0
CA D:TRP611 4.3 10.1 1.0
C D:SER633 4.4 12.5 1.0
N D:HIS615 4.4 12.0 1.0
ND1 D:HIS635 4.4 10.3 1.0
N D:GLY616 4.5 12.9 1.0
N D:HIS614 4.5 12.2 1.0
CA D:LEU634 4.5 12.5 1.0
CA D:HIS635 4.5 13.1 1.0
N D:HIS635 4.6 14.2 1.0
CG D:HIS635 4.7 13.6 1.0
O D:HOH901 4.7 15.4 1.0
N D:VAL613 4.8 14.1 1.0
CA D:HIS614 4.8 13.4 1.0
C D:VAL613 4.8 17.4 1.0
C D:HIS615 4.8 9.1 1.0
OH D:TYR631 4.8 14.7 1.0
CE1 D:HIS573 4.9 15.9 1.0
O D:TRP611 5.0 10.5 1.0
ND1 D:HIS573 5.0 14.2 1.0

Potassium binding site 8 out of 8 in 6dvn

Go back to Potassium Binding Sites List in 6dvn
Potassium binding site 8 out of 8 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ddk-137 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K803

b:22.5
occ:1.00
O D:PHE623 2.7 10.8 1.0
O D:VAL629 2.8 14.2 1.0
O D:HOH914 2.9 13.7 1.0
O D:ASP626 2.9 16.4 1.0
O D:TYR662 2.9 13.8 1.0
O D:HOH938 3.1 11.0 1.0
C D:TYR662 3.6 15.2 1.0
CB D:TYR662 3.6 14.7 1.0
C D:PHE623 3.7 15.0 1.0
CB D:PHE623 3.8 9.6 1.0
C D:VAL629 4.0 15.4 1.0
C D:ASP626 4.1 21.7 1.0
CA D:TYR662 4.3 15.8 1.0
N D:ASN663 4.3 14.6 1.0
N D:TYR631 4.4 10.8 1.0
CA D:PHE623 4.4 15.9 1.0
N D:ASP626 4.5 16.7 1.0
N D:GLU624 4.6 14.1 1.0
CA D:GLU624 4.6 17.5 1.0
CA D:LEU630 4.6 10.9 1.0
CA D:ASP626 4.7 23.1 1.0
CB D:TYR631 4.7 8.3 1.0
CA D:ASN663 4.7 13.1 1.0
CB D:ASN663 4.7 13.2 1.0
C D:GLU624 4.7 17.6 1.0
CB D:ASP626 4.8 17.5 1.0
O D:GLY659 4.8 19.2 1.0
O D:GLU624 4.8 11.8 1.0
N D:LEU630 4.8 12.4 1.0
CG D:TYR662 4.9 18.9 1.0
C D:LEU630 4.9 12.1 1.0

Reference:

N.J.Porter, J.D.Osko, D.Diedrich, T.Kurz, J.M.Hooker, F.K.Hansen, D.W.Christianson. Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J. Med. Chem. V. 61 8054 2018.
ISSN: ISSN 1520-4804
PubMed: 30118224
DOI: 10.1021/ACS.JMEDCHEM.8B01013
Page generated: Mon Dec 14 00:34:59 2020

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